Affymetrix Mouse Genome 430 2.0 arrays were used to compare transcript abundance in small intestines from germ-free (gf) and conventional (cv) mice, and from mice fed a normal diet vs a vitamin A-deficient diet. Differentially expressed transcripts were identified as outlined in ‘Materials and methods’, revealing 329 differentially-expressed genes between the germ-free and conventional groups, and 138 differentially-expressed genes between the vitamin A+ and vitamin A− groups. A Venn diagram representation of the experimental results is shown at left. 19 genes were differentially expressed in both comparisons and are displayed as a heatmap in which expression level is defined by Z-score (defined in ‘Materials and methods’). Saa1 and 2 are highlighted in blue. Other vitamin A-sensitive genes identified by this screen include granzymes A and B (gene symbols: GzmA and GzmB). There is a known role for retinoic acid in CD8+ T cell differentiation (Allie et al., 2013), which could explain the lowered abundance of granzyme transcripts in the vitamin A-deficient mice. Additionally, the array data reveal unexpected vitamin A-sensitive expression of three glycosyltransferases–fucosyltransferase 2 (Fut2), β1,6-N acetylglucosaminyltransferase (Gcnt1), and β1,3-galactosyltransferase 5 (B3galt5)–that participate in mucin glycan synthesis (Thomsson et al., 2002; Brockhausen et al., 2009).